S100P
Basic information
Region (hg38): 4:6693877-6697170
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100P gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 7 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 7 | 0 | 1 |
Variants in S100P
This is a list of pathogenic ClinVar variants found in the S100P region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-6693951-G-A | not specified | Uncertain significance (May 24, 2023) | ||
4-6693955-T-C | not specified | Uncertain significance (Mar 18, 2024) | ||
4-6693994-G-A | not specified | Uncertain significance (Mar 17, 2023) | ||
4-6694007-G-A | Benign (May 24, 2018) | |||
4-6694020-A-G | not specified | Uncertain significance (May 26, 2022) | ||
4-6694043-G-C | not specified | Uncertain significance (Jan 17, 2023) | ||
4-6696929-A-G | not specified | Uncertain significance (May 11, 2022) | ||
4-6696945-A-G | not specified | Uncertain significance (May 23, 2023) | ||
4-6697022-G-C | not specified | Uncertain significance (Aug 14, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
S100P | protein_coding | protein_coding | ENST00000296370 | 2 | 4102 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0333 | 0.630 | 125723 | 0 | 22 | 125745 | 0.0000875 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.378 | 63 | 55.1 | 1.14 | 0.00000302 | 624 |
Missense in Polyphen | 19 | 13.687 | 1.3881 | 170 | ||
Synonymous | 0.282 | 22 | 23.7 | 0.926 | 0.00000153 | 179 |
Loss of Function | 0.295 | 2 | 2.50 | 0.799 | 1.93e-7 | 20 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000361 | 0.0000352 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000588 | 0.000588 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May function as calcium sensor and contribute to cellular calcium signaling. In a calcium-dependent manner, functions by interacting with other proteins, such as EZR and PPP5C, and indirectly plays a role in physiological processes like the formation of microvilli in epithelial cells. May stimulate cell proliferation in an autocrine manner via activation of the receptor for activated glycation end products (RAGE). {ECO:0000269|PubMed:14617629, ECO:0000269|PubMed:19111582, ECO:0000269|PubMed:22399290}.;
- Pathway
- Gastric Cancer Network 1;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.222
- hipred
- N
- hipred_score
- 0.273
- ghis
- 0.560
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.947
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- response to organic substance;neutrophil degranulation;endothelial cell migration
- Cellular component
- extracellular region;nucleus;cytoplasm;nuclear body;microvillus membrane;secretory granule lumen;extracellular exosome
- Molecular function
- magnesium ion binding;calcium ion binding;protein binding;protein homodimerization activity;cadherin binding;transition metal ion binding;calcium-dependent protein binding;RAGE receptor binding